Type VII CRISPR proteins and systems

Abstract

The present application provides systems, methods and compositions used for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing. Novel nucleic acid targeting systems comprise components of Type VII Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems and transposable elements.

What is claimed is: 
     
         1 . An engineered system, comprising:
 a Type VII CRISPR effector protein,   wherein the Type VII CRISPR effector protein is capable of complexing with a crRNA to form a CRISPR-Cas complex, wherein the crRNA comprises a direct repeat (DR) sequence and a guide sequence capable of hybridizing to a target nucleic acid sequence, wherein the Type VII CRISPR effector does not have a REC1 domain, a REC2 domain, or both.   
     
     
         2 . The system of  claim 1 , wherein the Type VII CRISPR effector comprises a bridge helix domain, a RuvC domain or RuvC-like domain, and an insertion between the bridge helix and RuvC or RuvC-like domain, optionally wherein the insertion is capable of binding RNA. 
     
     
         3 . The system of  claim 2 , wherein the Type VII CRISPR effector comprises a RuvC I domain, a RuvC II domain, or both. 
     
     
         4 . The system of  claim 1 , wherein the Type VII CRISPR effector comprises an HNH domain. 
     
     
         5 . The system of  claim 1 , further comprising the crRNA. 
     
     
         6 . The system of  claim 1 , further comprising a tracr RNA and the CRISPR-Cas complex comprises the Type VII CRISPR effector protein complexed with the crRNA and the tracr RNA. 
     
     
         7 . The system of  claim 1 , further comprising two or more crRNAs. 
     
     
         8 . The system of  claim 1 , wherein the guide sequence is capable of hybridizing to a target nucleic acid in a prokaryotic cell or a target nucleic acid in a eukaryotic cell. 
     
     
         9 . The system of  claim 1 , wherein the Type VII CRISPR effector protein comprises one or more nuclear localization signals (NLSs). 
     
     
         10 . The system of  claim 1 , wherein the Type VII CRISPR effector protein is a nickase. 
     
     
         11 . The system of  claim 1 , wherein the Type VII CRISPR effector protein is catalytically inactive. 
     
     
         12 . The system of  claim 1 , wherein the Type VII CRISPR effector protein is coupled to or associated with one or more functional domains, optionally wherein the functional domain has methylase activity, demethylase activity, translation activation activity, translation initiation activity, translation repression activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, nuclease activity, single-strand RNA cleavage activity, double-strand RNA cleavage activity, single-strand DNA cleavage activity, double-strand DNA cleavage activity, molecular switch activity, chemical inducibility, light inducibility, nucleic acid binding activity, deaminase activity, or a combination thereof. 
     
     
         13 . The system of  claim 12 , wherein the functional domain cleaves the target nucleic acid, modifies transcription of the target nucleic acid, modifies translation of the target nucleic acid, or any combination thereof. 
     
     
         14 . The system of  claim 12 , wherein the functional domain comprises an adenosine deaminase, or catalytic domain thereof, or cytidine deaminase, or catalytic domain thereof. 
     
     
         15 . The system of  claim 14 , wherein the adenosine deaminase or catalytic domain thereof, comprises one or more mutations that increase activity or specificity of the adenosine deaminase relative to wild type. 
     
     
         16 . The system of  claim 15 , wherein the mutation confers an ability of the adenosine deaminase to deaminate cytidine. 
     
     
         17 . A method of modifying a target nucleic acid, the method comprising
 contacting the target nucleic acid with an engineered system of  claim 1 ,   wherein the guide sequence directs sequence-specific binding to the target nucleic acid sequence, whereby the target nucleic acid sequence, the expression of the target nucleic acid, or both is/are modified.   
     
     
         18 . The method of  claim 17 , wherein modifying occurs in vitro, ex vivo, or in vivo. 
     
     
         19 . The method of  claim 17 , wherein modifying the target nucleic acid comprises cleaving the target nucleic acid. 
     
     
         20 . The method of  claim 17 , wherein modifying expression of the target nucleic acid comprises increasing or decreasing transcription or translation of the target nucleic acid. 
     
     
         21 . The method of  claim 17 , wherein the target nucleic acid is in a prokaryotic cell or a eukaryotic cell, optionally wherein the eukaryotic cell is a mammalian cell or a human cell. 
     
     
         22 . A cell comprising: an engineered system as in  claim 1  or a vector system thereof. 
     
     
         23 . The cell of  claim 22 , wherein the cell is a prokaryotic cell or a eukaryotic cell, optionally wherein the eukaryotic cell is a mammalian cell or a human cell. 
     
     
         24 . A cell line of or comprising the cell according to  claim 22  or progeny thereof, optionally wherein the cell line comprises one or more polynucleotide modifications. 
     
     
         25 . A multicellular organism comprising one or more cells according to  claim 22 . 
     
     
         26 . A plant or animal model comprising one or more cells according to  claim 22 .